Personal tools

Coexpression cluster:C4236: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma |id=C4236 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma
|full_id=C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma
|gostat_on_coexpression_clusters=GO:0032357!oxidized purine DNA binding!3.29271505890964e-08!4436;2956$GO:0032356!oxidized DNA binding!3.29271505890964e-08!4436;2956$GO:0000400!four-way junction DNA binding!3.29271505890964e-08!4436;2956$GO:0032301!MutSalpha complex!3.29271505890964e-08!4436;2956$GO:0032143!single thymine insertion binding!3.29271505890964e-08!4436;2956$GO:0032139!dinucleotide insertion or deletion binding!4.93907258836446e-08!4436;2956$GO:0032134!mispaired DNA binding!4.93907258836446e-08!4436;2956$GO:0032137!guanine/thymine mispair binding!4.93907258836446e-08!4436;2956$GO:0032142!single guanine insertion binding!4.93907258836446e-08!4436;2956$GO:0032300!mismatch repair complex!4.93907258836446e-08!4436;2956$GO:0032135!DNA insertion or deletion binding!7.59857321286842e-08!4436;2956$GO:0032138!single base insertion or deletion binding!7.59857321286842e-08!4436;2956$GO:0000217!DNA secondary structure binding!7.59857321286842e-08!4436;2956$GO:0032405!MutLalpha complex binding!1.1759696638963e-07!4436;2956$GO:0032404!mismatch repair complex binding!3.073200721649e-07!4436;2956$GO:0043531!ADP binding!3.70430444127335e-07!4436;2956$GO:0006284!base-excision repair!5.76225135309188e-06!4436;2956$GO:0003684!damaged DNA binding!1.07562025257715e-05!4436;2956$GO:0030983!mismatched DNA binding!2.09260707033337e-05!4436;2956$GO:0006298!mismatch repair!2.29392482437372e-05!4436;2956$GO:0045005!maintenance of fidelity during DNA-dependent DNA replication!2.29392482437372e-05!4436;2956$GO:0032403!protein complex binding!3.77913887443039e-05!4436;2956$GO:0003690!double-stranded DNA binding!4.13593643703911e-05!4436;2956$GO:0043566!structure-specific DNA binding!8.61662371978417e-05!4436;2956$GO:0006261!DNA-dependent DNA replication!8.91008694940949e-05!4436;2956$GO:0006260!DNA replication!0.000372850589695633!4436;2956$GO:0032302!MutSbeta complex!0.000372850589695633!4436$GO:0000701!purine-specific mismatch base pair DNA N-glycosylase activity!0.000372850589695633!2956$GO:0043570!maintenance of DNA repeat elements!0.000372850589695633!4436$GO:0032181!dinucleotide repeat insertion binding!0.000372850589695633!4436$GO:0006281!DNA repair!0.000407000824604192!4436;2956$GO:0000287!magnesium ion binding!0.000493471458313944!4436;2956$GO:0006974!response to DNA damage stimulus!0.000493471458313944!4436;2956$GO:0000700!mismatch base pair DNA N-glycosylase activity!0.000493471458313944!2956$GO:0009719!response to endogenous stimulus!0.000656924877524407!4436;2956$GO:0016887!ATPase activity!0.000903237472812511!4436;2956$GO:0006301!postreplication repair!0.00105801164303689!4436$GO:0017111!nucleoside-triphosphatase activity!0.00216842616708457!4436;2956$GO:0016462!pyrophosphatase activity!0.00224103793111858!4436;2956$GO:0016818!hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides!0.00224103793111858!4436;2956$GO:0016817!hydrolase activity, acting on acid anhydrides!0.00224103793111858!4436;2956$GO:0019104!DNA N-glycosylase activity!0.00234808105336975!2956$GO:0044428!nuclear part!0.00234808105336975!4436;2956$GO:0006950!response to stress!0.00279144035012888!4436;2956$GO:0006259!DNA metabolic process!0.00285140343528084!4436;2956$GO:0016799!hydrolase activity, hydrolyzing N-glycosyl compounds!0.00291701627068806!2956$GO:0003697!single-stranded DNA binding!0.00725238356455489!4436$GO:0008022!protein C-terminus binding!0.00861303260242305!4436$GO:0005524!ATP binding!0.0130414729973987!4436;2956$GO:0032559!adenyl ribonucleotide binding!0.0130414729973987!4436;2956$GO:0043234!protein complex!0.0134110444302739!4436;2956$GO:0030554!adenyl nucleotide binding!0.0136319828171337!4436;2956$GO:0042803!protein homodimerization activity!0.0166344703124406!4436$GO:0003677!DNA binding!0.0181049202533107!4436;2956$GO:0032553!ribonucleotide binding!0.0181049202533107!4436;2956$GO:0032555!purine ribonucleotide binding!0.0181049202533107!4436;2956$GO:0017076!purine nucleotide binding!0.0191399749681331!4436;2956$GO:0016798!hydrolase activity, acting on glycosyl bonds!0.020879621687379!2956$GO:0032991!macromolecular complex!0.020879621687379!4436;2956$GO:0045786!negative regulation of progression through cell cycle!0.020879621687379!4436$GO:0016787!hydrolase activity!0.020879621687379!4436;2956$GO:0044446!intracellular organelle part!0.0222817113393344!4436;2956$GO:0044422!organelle part!0.0222817113393344!4436;2956$GO:0000166!nucleotide binding!0.0233801187807446!4436;2956$GO:0000074!regulation of progression through cell cycle!0.029940926774321!4436$GO:0051726!regulation of cell cycle!0.029940926774321!4436$GO:0042802!identical protein binding!0.029940926774321!4436$GO:0046983!protein dimerization activity!0.029940926774321!4436$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0407929887479537!4436;2956$GO:0051276!chromosome organization and biogenesis!0.0424879627039622!4436$GO:0005634!nucleus!0.0425424652209084!4436;2956$GO:0003676!nucleic acid binding!0.0464864505909484!4436;2956$GO:0022402!cell cycle process!0.047444133633493!4436
|id=C4236
|id=C4236
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr2:47630255..47630333,+p1@MSH2
Hg19::chr2:48010276..48010307,+p1@MSH6
Hg19::chr2:48010312..48010328,+p2@MSH6


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0032357oxidized purine DNA binding3.29271505890964e-08
GO:0032356oxidized DNA binding3.29271505890964e-08
GO:0000400four-way junction DNA binding3.29271505890964e-08
GO:0032301MutSalpha complex3.29271505890964e-08
GO:0032143single thymine insertion binding3.29271505890964e-08
GO:0032139dinucleotide insertion or deletion binding4.93907258836446e-08
GO:0032134mispaired DNA binding4.93907258836446e-08
GO:0032137guanine/thymine mispair binding4.93907258836446e-08
GO:0032142single guanine insertion binding4.93907258836446e-08
GO:0032300mismatch repair complex4.93907258836446e-08
GO:0032135DNA insertion or deletion binding7.59857321286842e-08
GO:0032138single base insertion or deletion binding7.59857321286842e-08
GO:0000217DNA secondary structure binding7.59857321286842e-08
GO:0032405MutLalpha complex binding1.1759696638963e-07
GO:0032404mismatch repair complex binding3.073200721649e-07
GO:0043531ADP binding3.70430444127335e-07
GO:0006284base-excision repair5.76225135309188e-06
GO:0003684damaged DNA binding1.07562025257715e-05
GO:0030983mismatched DNA binding2.09260707033337e-05
GO:0006298mismatch repair2.29392482437372e-05
GO:0045005maintenance of fidelity during DNA-dependent DNA replication2.29392482437372e-05
GO:0032403protein complex binding3.77913887443039e-05
GO:0003690double-stranded DNA binding4.13593643703911e-05
GO:0043566structure-specific DNA binding8.61662371978417e-05
GO:0006261DNA-dependent DNA replication8.91008694940949e-05
GO:0006260DNA replication0.000372850589695633
GO:0032302MutSbeta complex0.000372850589695633
GO:0000701purine-specific mismatch base pair DNA N-glycosylase activity0.000372850589695633
GO:0043570maintenance of DNA repeat elements0.000372850589695633
GO:0032181dinucleotide repeat insertion binding0.000372850589695633
GO:0006281DNA repair0.000407000824604192
GO:0000287magnesium ion binding0.000493471458313944
GO:0006974response to DNA damage stimulus0.000493471458313944
GO:0000700mismatch base pair DNA N-glycosylase activity0.000493471458313944
GO:0009719response to endogenous stimulus0.000656924877524407
GO:0016887ATPase activity0.000903237472812511
GO:0006301postreplication repair0.00105801164303689
GO:0017111nucleoside-triphosphatase activity0.00216842616708457
GO:0016462pyrophosphatase activity0.00224103793111858
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.00224103793111858
GO:0016817hydrolase activity, acting on acid anhydrides0.00224103793111858
GO:0019104DNA N-glycosylase activity0.00234808105336975
GO:0044428nuclear part0.00234808105336975
GO:0006950response to stress0.00279144035012888
GO:0006259DNA metabolic process0.00285140343528084
GO:0016799hydrolase activity, hydrolyzing N-glycosyl compounds0.00291701627068806
GO:0003697single-stranded DNA binding0.00725238356455489
GO:0008022protein C-terminus binding0.00861303260242305
GO:0005524ATP binding0.0130414729973987
GO:0032559adenyl ribonucleotide binding0.0130414729973987
GO:0043234protein complex0.0134110444302739
GO:0030554adenyl nucleotide binding0.0136319828171337
GO:0042803protein homodimerization activity0.0166344703124406
GO:0003677DNA binding0.0181049202533107
GO:0032553ribonucleotide binding0.0181049202533107
GO:0032555purine ribonucleotide binding0.0181049202533107
GO:0017076purine nucleotide binding0.0191399749681331
GO:0016798hydrolase activity, acting on glycosyl bonds0.020879621687379
GO:0032991macromolecular complex0.020879621687379
GO:0045786negative regulation of progression through cell cycle0.020879621687379
GO:0016787hydrolase activity0.020879621687379
GO:0044446intracellular organelle part0.0222817113393344
GO:0044422organelle part0.0222817113393344
GO:0000166nucleotide binding0.0233801187807446
GO:0000074regulation of progression through cell cycle0.029940926774321
GO:0051726regulation of cell cycle0.029940926774321
GO:0042802identical protein binding0.029940926774321
GO:0046983protein dimerization activity0.029940926774321
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0407929887479537
GO:0051276chromosome organization and biogenesis0.0424879627039622
GO:0005634nucleus0.0425424652209084
GO:0003676nucleic acid binding0.0464864505909484
GO:0022402cell cycle process0.047444133633493



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4236&oldid=1703187"